Summary of Study ST001489

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001006. The data can be accessed directly via it's Project DOI: 10.21228/M8NT36 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001489
Study Title	Metabolomics by UHPLC-HRMS reveals the impact of heat stress on pathogen-elicited immunity in maize
Study Summary	Studies investigating crop resistance to biotic and abiotic stress have largely focused on plant responses to singular forms of stress and individual biochemical pathways that only partially represent stress responses. Thus, combined biotic and abiotic stress treatments and the global assessment of their elicited metabolic expression remains largely unexplored. In this study, we employed targeted and untargeted metabolomics to investigate the metabolic responses of maize (Zea mays) to both individual and combinatorial stress treatments using heat (abiotic) and Cochliobolus heterostrophus infection (biotic) experiments. Ultra-high-performance liquid chromatography-high-resolution mass spectrometry revealed significant metabolic responses to C. heterostrophus infection and heat stress, and comparative analyses between these individual forms of stress demonstrated differential elicitation between the two global metabolomes. In combinatorial experiments, treatment with heat stress prior to fungal inoculation negatively impacted maize disease resistance against C. heterostrophus, and distinct metabolome separation between combinatorial stressed plants and the non-heat stressed infected controls was observed. Targeted analysis revealed inducible primary and secondary metabolite responses to biotic/abiotic stress, and combinatorial experiments indicated that deficiency in the hydroxycinnamic acid, p-coumaric acid, may lead to the heat-induced susceptibility of maize to C. heterostrophus. Collectively, these findings demonstrate that abiotic stress can predispose crops to more severe disease symptoms, underlining the increasing need to investigate defense chemistry in plants under combinatorial stress.
Institute	Agricultural Research Service, United States Department of Agriculture
Department	Center of Medical, Agricultural, and Veterinary Entomology
Laboratory	Chemistry Research Unit
Last Name	Christensen
First Name	Shawn
Address	1600 SW 23rd Drive Gainesville, FL 32608
Email	shawn.christensen@usda.gov
Phone	3523745739
Submit Date	2020-08-03
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2021-08-03
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001006
Project DOI:	doi: 10.21228/M8NT36
Project Title:	Metabolomics by UHPLC-HRMS reveals the impact of heat stress on pathogen-elicited immunity in maize
Project Summary:	Studies investigating crop resistance to biotic and abiotic stress have largely focused on plant responses to singular forms of stress and individual biochemical pathways that only partially represent stress responses. Thus, combined biotic and abiotic stress treatments and the global assessment of their elicited metabolic expression remains largely unexplored. In this study, we employed targeted and untargeted metabolomics to investigate the metabolic responses of maize (Zea mays) to both individual and combinatorial stress treatments using heat (abiotic) and Cochliobolus heterostrophus infection (biotic) experiments. Ultra-high-performance liquid chromatography-high-resolution mass spectrometry revealed significant metabolic responses to C. heterostrophus infection and heat stress, and comparative analyses between these individual forms of stress demonstrated differential elicitation between the two global metabolomes. In combinatorial experiments, treatment with heat stress prior to fungal inoculation negatively impacted maize disease resistance against C. heterostrophus, and distinct metabolome separation between combinatorial stressed plants and the non-heat stressed infected controls was observed. Targeted analysis revealed inducible primary and secondary metabolite responses to biotic/abiotic stress, and combinatorial experiments indicated that deficiency in the hydroxycinnamic acid, p-coumaric acid, may lead to the heat-induced susceptibility of maize to C. heterostrophus. Collectively, these findings demonstrate that abiotic stress can predispose crops to more severe disease symptoms, underlining the increasing need to investigate defense chemistry in plants under combinatorial stress.
Institute:	Agricultural Research Service, United States Department of Agriculture
Last Name:	Christensen
First Name:	Shawn
Address:	1600 SW 23rd Drive Gainesville, FL 32608, Gainesville, Florida, 32607, USA
Email:	shawn.christensen@usda.gov
Phone:	3523745739

Subject:

Subject ID:	SU001563
Subject Type:	Plant
Subject Species:	Zea mays
Taxonomy ID:	4577

Factors:

Subject type: Plant; Subject species: Zea mays (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample Type	Age	Growth Temperature
SA125415	8_	Control	14 day	28
SA125416	9_	Control	14 day	28
SA125417	12_	Control	14 day	28
SA125418	7_	Control	14 day	28
SA125419	10_	Control	14 day	28
SA125420	11_	Control	14 day	28
SA125421	31_	Control	14 day	38 returned to 28
SA125422	32_	Control	14 day	38 returned to 28
SA125423	33_	Control	14 day	38 returned to 28
SA125424	34_	Control	14 day	38 returned to 28
SA125425	56_	Control	14 day	38 returned to 38
SA125426	57_	Control	14 day	38 returned to 38
SA125427	58_	Control	14 day	38 returned to 38
SA125428	55_	Control	14 day	38 returned to 38
SA125429	59_	Control	14 day	38 returned to 38
SA125430	4_	SLB inoculation	14 day	28
SA125431	5_	SLB inoculation	14 day	28
SA125432	2_	SLB inoculation	14 day	28
SA125433	1_	SLB inoculation	14 day	28
SA125434	6_	SLB inoculation	14 day	28
SA125435	3_	SLB inoculation	14 day	28
SA125436	29_	SLB inoculation	14 day	38 returned to 28
SA125437	28_	SLB inoculation	14 day	38 returned to 28
SA125438	27_	SLB inoculation	14 day	38 returned to 28
SA125439	26_	SLB inoculation	14 day	38 returned to 28
SA125440	25_	SLB inoculation	14 day	38 returned to 28
SA125441	30_	SLB inoculation	14 day	38 returned to 28
SA125442	49_	SLB inoculation	14 day	38 returned to 38
SA125443	51_	SLB inoculation	14 day	38 returned to 38
SA125444	52_	SLB inoculation	14 day	38 returned to 38
SA125445	53_	SLB inoculation	14 day	38 returned to 38
SA125446	54_	SLB inoculation	14 day	38 returned to 38
SA125447	50_	SLB inoculation	14 day	38 returned to 38

Showing results 1 to 33 of 33

Showing results 1 to 33 of 33

Collection:

Collection ID:	CO001558
Collection Summary:	Samples were collected and flash frozen in liquid N2
Sample Type:	Plant

Treatment:

Treatment ID:	TR001578
Treatment Summary:	For inoculations, single isolates of Cochliobolus heterostrophus were cultured on V8 agar for 3-4 weeks as described by (Christensen et al., 2018). Spot inoculations were performed on 14-d-old plants in which four 10 μl droplets of either C. heterostrophus suspension (1x106 spores mL-1) or control solution (sterile 0.1% Tween 20) were applied in a staggered fashion (Fig. 2a and Fig. 4a) onto the middle portion of the third leaf about 10cm from the distal tip. Following inoculation, both heat-stressed and non-heat-stressed plants were placed in a plastic humidity chamber and placed in the 28°C Percival. At 24 hours post-inoculation, infected and non-infected controls were removed from the humidity chambers and maintained at 28°C for the remainder of the experiment. At 72 hours post-inoculation, leaves (n=6) were photographed and immediately harvested into liquid N2. Lesions were digitally measured using ImageJ software (ImageJ 1.36b; Wayne Rasband, NIH, Bethesda, MD, USA).

Treatment ID:

TR001578

Treatment Summary:

For inoculations, single isolates of Cochliobolus heterostrophus were cultured on V8 agar for 3-4 weeks as described by (Christensen et al., 2018). Spot inoculations were performed on 14-d-old plants in which four 10 μl droplets of either C. heterostrophus suspension (1x106 spores mL-1) or control solution (sterile 0.1% Tween 20) were applied in a staggered fashion (Fig. 2a and Fig. 4a) onto the middle portion of the third leaf about 10cm from the distal tip. Following inoculation, both heat-stressed and non-heat-stressed plants were placed in a plastic humidity chamber and placed in the 28°C Percival. At 24 hours post-inoculation, infected and non-infected controls were removed from the humidity chambers and maintained at 28°C for the remainder of the experiment. At 72 hours post-inoculation, leaves (n=6) were photographed and immediately harvested into liquid N2. Lesions were digitally measured using ImageJ software (ImageJ 1.36b; Wayne Rasband, NIH, Bethesda, MD, USA).

Sample Preparation:

Sampleprep ID:	SP001571
Sampleprep Summary:	LCMS grade reagents (Thermo Fisher Scientific) were used throughout the extraction. Frozen 1.5-mL fast prep tubes with Zirmil® beads (1.1mm; SEPR Ceramic Beads and Powders, Mountainside, NJ, USA) containing 50 mg of ground and frozen tissue were carefully thawed to 4°C then transferred to ice. An internal standard mix of 12 μL containing caffeine, D6-Abscisic acid, D5-Jasmonic acid, D5-Cinnamic acid, D5-Indole-3-acetic acid, 13C-alpha linolenic acid, and nicotine at 8.33 μg/mL was added to each sample along with 750 μL of 10 mM of ammonium acetate and 750 μL of methanol (MeOH). Samples were mixed by vortex then homogenized at 6000 RPM for 30 seconds in a FastPrep® FP 120 tissue homogenizer (Qbiogene) and then sonicated in an ambient water bath for 15 min. Samples were centrifuged for 10 minutes at 20,000 RCF at ambient temperature, then 1 mL of supernatant was transferred to individual 4 mL glass vials. The supernatant was dried under a nitrogen stream at 30°C, reconstituted in 200 μL of 0.1% formic acid in water, and vortexed for 30 seconds. Vial contents were transferred to a 1.5-mL snap-cap tube, placed on ice for 10 minutes, then centrifuged at 20,000 RCF for 10 minutes at ambient temperature. 150 μL of supernatant was transferred to glass LC vials for UHPLC-HRMS analysis.

Sampleprep ID:

SP001571

Sampleprep Summary:

LCMS grade reagents (Thermo Fisher Scientific) were used throughout the extraction. Frozen 1.5-mL fast prep tubes with Zirmil® beads (1.1mm; SEPR Ceramic Beads and Powders, Mountainside, NJ, USA) containing 50 mg of ground and frozen tissue were carefully thawed to 4°C then transferred to ice. An internal standard mix of 12 μL containing caffeine, D6-Abscisic acid, D5-Jasmonic acid, D5-Cinnamic acid, D5-Indole-3-acetic acid, 13C-alpha linolenic acid, and nicotine at 8.33 μg/mL was added to each sample along with 750 μL of 10 mM of ammonium acetate and 750 μL of methanol (MeOH). Samples were mixed by vortex then homogenized at 6000 RPM for 30 seconds in a FastPrep® FP 120 tissue homogenizer (Qbiogene) and then sonicated in an ambient water bath for 15 min. Samples were centrifuged for 10 minutes at 20,000 RCF at ambient temperature, then 1 mL of supernatant was transferred to individual 4 mL glass vials. The supernatant was dried under a nitrogen stream at 30°C, reconstituted in 200 μL of 0.1% formic acid in water, and vortexed for 30 seconds. Vial contents were transferred to a 1.5-mL snap-cap tube, placed on ice for 10 minutes, then centrifuged at 20,000 RCF for 10 minutes at ambient temperature. 150 μL of supernatant was transferred to glass LC vials for UHPLC-HRMS analysis.

Combined analysis:

Analysis ID	AN002466	AN002467
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)	ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	peak intensity	peak intensity

Chromatography:

Chromatography ID:	CH001808
Instrument Name:	Thermo Vanquish
Column Name:	ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002286
Analysis ID:	AN002466
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The raw acquisition data were processed using a similar workflow described in previous work (Chamberlain et al., 2019a, b), which we detail here. Raw data files were converted from .raw to .mzxml format using RawConverter (He et al., 2015). MZmine 2 was used for processing the raw data including detecting masses, building chromatograms, grouping isotopic peaks, removing duplicate peaks, and aligning features (Pluskal et al., 2010). Identification was assigned to features by m/z (≤5 ppm) and retention time (0.2 min) (level 1 – identified compounds according to Metabolomics Standards Initiative standards (Sumner et al., 2007)) matching tousing our method-specific metabolite library produced from pure standards previously analyzed using this the above-mentioned chromatographic gradient. Processed data were exported from MZmine as a feature list containing the signal intensity for each feature in each sample. A small value (half the minimum value in the dataset) was used to replace zeros (no detection). The data were filtered to remove sample features with  10% signal contribution from their corresponding features in the extraction blanks. From this point, the data were further processed, normalized, and filtered using MetaboAnalyst 4.0 (Chong et al., 2018). For whole-metabolome comparative analyses, the data were normalized to total ion signal and feature intensities were auto-scaled to facilitate statistical comparisons (van den Berg et al., 2006). Statistical significance, defined as p  0.05, was determined using the two-tailed student’s t-test, and values for significance were adjusted for the false discovery rate with the Bonferroni-Holm method (HOLM, 1979).
Ion Mode:	POSITIVE

MS ID:	MS002287
Analysis ID:	AN002467
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The raw acquisition data were processed using a similar workflow described in previous work (Chamberlain et al., 2019a, b), which we detail here. Raw data files were converted from .raw to .mzxml format using RawConverter (He et al., 2015). MZmine 2 was used for processing the raw data including detecting masses, building chromatograms, grouping isotopic peaks, removing duplicate peaks, and aligning features (Pluskal et al., 2010). Identification was assigned to features by m/z (≤5 ppm) and retention time (0.2 min) (level 1 – identified compounds according to Metabolomics Standards Initiative standards (Sumner et al., 2007)) matching tousing our method-specific metabolite library produced from pure standards previously analyzed using this the above-mentioned chromatographic gradient. Processed data were exported from MZmine as a feature list containing the signal intensity for each feature in each sample. A small value (half the minimum value in the dataset) was used to replace zeros (no detection). The data were filtered to remove sample features with  10% signal contribution from their corresponding features in the extraction blanks. From this point, the data were further processed, normalized, and filtered using MetaboAnalyst 4.0 (Chong et al., 2018). For whole-metabolome comparative analyses, the data were normalized to total ion signal and feature intensities were auto-scaled to facilitate statistical comparisons (van den Berg et al., 2006). Statistical significance, defined as p  0.05, was determined using the two-tailed student’s t-test, and values for significance were adjusted for the false discovery rate with the Bonferroni-Holm method (HOLM, 1979).
Ion Mode:	NEGATIVE